[{"date_created":"2023-09-03T22:01:14Z","department":[{"_id":"RoSe"}],"author":[{"first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert"},{"last_name":"Solovej","full_name":"Solovej, Jan Philip","first_name":"Jan Philip"}],"doi":"10.1016/j.jfa.2023.110129","has_accepted_license":"1","_id":"14254","scopus_import":"1","issue":"10","acknowledgement":"J.P.S. thanks the Institute of Science and Technology Austria for the hospitality and support during a visit where this work was done. J.P.S. was also partially supported by the VILLUM Centre of Excellence for the Mathematics of Quantum Theory (QMATH) (grant No. 10059).","language":[{"iso":"eng"}],"file_date_updated":"2024-01-30T14:15:16Z","corr_author":"1","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"110129","isi":1,"month":"11","type":"journal_article","external_id":{"arxiv":["2303.04504"],"isi":["001071552300001"]},"quality_controlled":"1","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"intvolume":"       285","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Elsevier","oa":1,"volume":285,"article_type":"original","citation":{"mla":"Seiringer, Robert, and Jan Philip Solovej. “A Simple Approach to Lieb-Thirring Type Inequalities.” <i>Journal of Functional Analysis</i>, vol. 285, no. 10, 110129, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">10.1016/j.jfa.2023.110129</a>.","short":"R. Seiringer, J.P. Solovej, Journal of Functional Analysis 285 (2023).","ieee":"R. Seiringer and J. P. Solovej, “A simple approach to Lieb-Thirring type inequalities,” <i>Journal of Functional Analysis</i>, vol. 285, no. 10. Elsevier, 2023.","ista":"Seiringer R, Solovej JP. 2023. A simple approach to Lieb-Thirring type inequalities. Journal of Functional Analysis. 285(10), 110129.","chicago":"Seiringer, Robert, and Jan Philip Solovej. “A Simple Approach to Lieb-Thirring Type Inequalities.” <i>Journal of Functional Analysis</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">https://doi.org/10.1016/j.jfa.2023.110129</a>.","apa":"Seiringer, R., &#38; Solovej, J. P. (2023). A simple approach to Lieb-Thirring type inequalities. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">https://doi.org/10.1016/j.jfa.2023.110129</a>","ama":"Seiringer R, Solovej JP. A simple approach to Lieb-Thirring type inequalities. <i>Journal of Functional Analysis</i>. 2023;285(10). doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">10.1016/j.jfa.2023.110129</a>"},"file":[{"file_id":"14915","file_name":"2023_JourFunctionalAnalysis_Seiringer.pdf","checksum":"28e424ad91be6219e9d321054ce3a412","date_created":"2024-01-30T14:15:16Z","content_type":"application/pdf","creator":"dernst","success":1,"relation":"main_file","file_size":232934,"access_level":"open_access","date_updated":"2024-01-30T14:15:16Z"}],"abstract":[{"text":"In [10] Nam proved a Lieb–Thirring Inequality for the kinetic energy of a fermionic quantum system, with almost optimal (semi-classical) constant and a gradient correction term. We present a stronger version of this inequality, with a much simplified proof. As a corollary we obtain a simple proof of the original Lieb–Thirring inequality.","lang":"eng"}],"arxiv":1,"title":"A simple approach to Lieb-Thirring type inequalities","ddc":["510"],"date_published":"2023-11-15T00:00:00Z","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","date_updated":"2024-10-09T21:06:47Z","day":"15","status":"public","publication":"Journal of Functional Analysis","publication_status":"published"},{"quality_controlled":"1","month":"08","type":"journal_article","external_id":{"pmid":["37578957"],"isi":["001050846300004"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"publisher":"Public Library of Science","volume":19,"publication_identifier":{"eissn":["1553-7374"],"issn":["1553-7366"]},"intvolume":"        19","article_type":"original","project":[{"name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","call_identifier":"FWF"}],"pmid":1,"citation":{"short":"J. Koch, Q. Xin, M. Obr, A. Schäfer, N. Rolfs, H.A. Anagho, A. Kudulyte, L. Woltereck, S. Kummer, J. Campos, Z.M. Uckeley, L. Bell-Sakyi, H.G. Kräusslich, F.K. Schur, C. Acuna, P.Y. Lozach, PLoS Pathogens 19 (2023).","mla":"Koch, Jana, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” <i>PLoS Pathogens</i>, vol. 19, no. 8, e1011562, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1011562\">10.1371/journal.ppat.1011562</a>.","chicago":"Koch, Jana, Qilin Xin, Martin Obr, Alicia Schäfer, Nina Rolfs, Holda A. Anagho, Aiste Kudulyte, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” <i>PLoS Pathogens</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.ppat.1011562\">https://doi.org/10.1371/journal.ppat.1011562</a>.","ista":"Koch J, Xin Q, Obr M, Schäfer A, Rolfs N, Anagho HA, Kudulyte A, Woltereck L, Kummer S, Campos J, Uckeley ZM, Bell-Sakyi L, Kräusslich HG, Schur FK, Acuna C, Lozach PY. 2023. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. 19(8), e1011562.","ieee":"J. Koch <i>et al.</i>, “The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells,” <i>PLoS Pathogens</i>, vol. 19, no. 8. Public Library of Science, 2023.","apa":"Koch, J., Xin, Q., Obr, M., Schäfer, A., Rolfs, N., Anagho, H. A., … Lozach, P. Y. (2023). The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. <i>PLoS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1011562\">https://doi.org/10.1371/journal.ppat.1011562</a>","ama":"Koch J, Xin Q, Obr M, et al. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. <i>PLoS Pathogens</i>. 2023;19(8). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1011562\">10.1371/journal.ppat.1011562</a>"},"file":[{"file_size":4458336,"access_level":"open_access","date_updated":"2023-09-06T06:41:52Z","success":1,"relation":"main_file","date_created":"2023-09-06T06:41:52Z","content_type":"application/pdf","creator":"dernst","file_id":"14269","checksum":"47ca3bb54b27f28b05644be0ad064bc6","file_name":"2023_PloSPathogens_Koch.pdf"}],"abstract":[{"lang":"eng","text":"Toscana virus is a major cause of arboviral disease in humans in the Mediterranean basin during summer. However, early virus-host cell interactions and entry mechanisms remain poorly characterized. Investigating iPSC-derived human neurons and cell lines, we found that virus binding to the cell surface was specific, and 50% of bound virions were endocytosed within 10 min. Virions entered Rab5a+ early endosomes and, subsequently, Rab7a+ and LAMP-1+ late endosomal compartments. Penetration required intact late endosomes and occurred within 30 min following internalization. Virus entry relied on vacuolar acidification, with an optimal pH for viral membrane fusion at pH 5.5. The pH threshold increased to 5.8 with longer pre-exposure of virions to the slightly acidic pH in early endosomes. Strikingly, the particles remained infectious after entering late endosomes with a pH below the fusion threshold. Overall, our study establishes Toscana virus as a late-penetrating virus and reveals an atypical use of vacuolar acidity by this virus to enter host cells."}],"title":"The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells","ddc":["570"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"}],"day":"14","date_updated":"2025-04-15T08:24:50Z","date_published":"2023-08-14T00:00:00Z","article_processing_charge":"Yes","publication":"PLoS Pathogens","status":"public","publication_status":"published","author":[{"first_name":"Jana","full_name":"Koch, Jana","last_name":"Koch"},{"full_name":"Xin, Qilin","last_name":"Xin","first_name":"Qilin"},{"first_name":"Martin","orcid":"0000-0003-1756-6564","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","full_name":"Obr, Martin"},{"first_name":"Alicia","last_name":"Schäfer","full_name":"Schäfer, Alicia"},{"first_name":"Nina","last_name":"Rolfs","full_name":"Rolfs, Nina"},{"full_name":"Anagho, Holda A.","last_name":"Anagho","first_name":"Holda A."},{"first_name":"Aiste","last_name":"Kudulyte","full_name":"Kudulyte, Aiste"},{"full_name":"Woltereck, Lea","last_name":"Woltereck","first_name":"Lea"},{"first_name":"Susann","full_name":"Kummer, Susann","last_name":"Kummer"},{"first_name":"Joaquin","full_name":"Campos, Joaquin","last_name":"Campos"},{"full_name":"Uckeley, Zina M.","last_name":"Uckeley","first_name":"Zina M."},{"last_name":"Bell-Sakyi","full_name":"Bell-Sakyi, Lesley","first_name":"Lesley"},{"full_name":"Kräusslich, Hans Georg","last_name":"Kräusslich","first_name":"Hans Georg"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian Km","first_name":"Florian Km","orcid":"0000-0003-4790-8078"},{"full_name":"Acuna, Claudio","last_name":"Acuna","first_name":"Claudio"},{"first_name":"Pierre Yves","full_name":"Lozach, Pierre Yves","last_name":"Lozach"}],"department":[{"_id":"FlSc"}],"date_created":"2023-09-03T22:01:14Z","_id":"14255","has_accepted_license":"1","doi":"10.1371/journal.ppat.1011562","issue":"8","acknowledgement":"We acknowledge Elodie Chatre and the Imaging Platform Platim, SFR Biosciences, Lyon, as well as Vibor Laketa and the Infectious Diseases Imaging Platform (IDIP) at the Center for Integrative Infectious Disease Research (CIID) Heidelberg. The sand fly cell lines were supplied by the Tick Cell Biobank at the University of Liverpool. F.K.M.S. acknowledges support from the Scientific Service Units (SSUs) of ISTA through resources provided by the Electron Microscopy Facility (EMF).\r\nThis work was supported by CellNetworks Research Group funds and Deutsche Forschungsgemeinschaft (DFG) funding (LO-2338/3-1) and the Agence Nationale de la Recherche (ANR) funding (grant numbers ANR-21-CE11-0012 and ANR-22-CE15-0034), all awarded to P.-Y.L. This work was also supported by the LABEX ECOFECT (ANR-11-LABX-0048) of Université de Lyon (UDL), within the program “Investissements d’Avenir” (ANR-11-IDEX-0007) operated by the ANR and by the RESPOND program of the UDL (awarded to P.-Y.L) . C.A. was supported by the Chica and Heinz Schaller Research Group funds, NARSAD 2019 award, a Fritz Thyssen Research Grant, and the SFB1158-S02 grant. L.B-S. is supported by a United Kingdom Biotechnology and Biological Sciences Research Council grant (BB/P024270/1) and a Wellcome Trust grant (223743/Z/21/Z). F.K.M.S acknowledges support from the Austrian Science Fund (FWF, P31445). J.K. received a salary from the DFG (LO-2338/3-1) and then from the ANR (ANR-11-LABX-0048). The salary of Z.M.U. was partially covered by the DFG (LO-2338/3-1). S.K. received a salary from the DFG (SFB1129). We are grateful to the Chinese Scholarship Council (CSC; 201904910701), DAAD/ANID (57451854/62180003), the Rufus A. Kellogg fellowship program (Amherst College, Massachusetts, USA) for awarding fellowships to Q.X., J.C., and H.A.A., respectively.","scopus_import":"1","language":[{"iso":"eng"}],"file_date_updated":"2023-09-06T06:41:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e1011562","isi":1,"year":"2023"},{"author":[{"first_name":"Sven E.","last_name":"Ojavee","full_name":"Ojavee, Sven E."},{"full_name":"Darrous, Liza","last_name":"Darrous","first_name":"Liza"},{"full_name":"Patxot, Marion","last_name":"Patxot","first_name":"Marion"},{"full_name":"Läll, Kristi","last_name":"Läll","first_name":"Kristi"},{"first_name":"Krista","last_name":"Fischer","full_name":"Fischer, Krista"},{"full_name":"Mägi, Reedik","last_name":"Mägi","first_name":"Reedik"},{"full_name":"Kutalik, Zoltan","last_name":"Kutalik","first_name":"Zoltan"},{"full_name":"Robinson, Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard"}],"date_created":"2023-09-03T22:01:15Z","department":[{"_id":"MaRo"}],"acknowledgement":"This project was funded by an SNSF Eccellenza grant to M.R.R. (PCEGP3-181181) and by core funding from the Institute of Science and Technology Austria. K.L. and R.M. were supported by the Estonian Research Council grant 1911. Estonian Biobank computations were performed in the High-Performance Computing Center, University of Tartu. We thank Triin Laisk for her valuable insights and comments that helped greatly. We would like to acknowledge the participants and investigators of UK Biobank and Estonian Biobank studies. This project uses UK Biobank data under project number 35520.","issue":"9","scopus_import":"1","_id":"14258","has_accepted_license":"1","doi":"10.1016/j.ajhg.2023.07.006","corr_author":"1","file_date_updated":"2024-01-30T13:20:35Z","language":[{"iso":"eng"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2023","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"volume":110,"publisher":"Elsevier","intvolume":"       110","publication_identifier":{"eissn":["1537-6605"],"issn":["0002-9297"]},"quality_controlled":"1","type":"journal_article","month":"09","external_id":{"isi":["001074842500001"],"pmid":["37543033"]},"page":"1549-1563","file":[{"relation":"main_file","success":1,"date_updated":"2024-01-30T13:20:35Z","access_level":"open_access","file_size":2551276,"checksum":"4108b031dc726ae6b4a5ae7e021ba188","file_name":"2023_AJHG_Ojavee.pdf","file_id":"14912","creator":"dernst","content_type":"application/pdf","date_created":"2024-01-30T13:20:35Z"}],"pmid":1,"citation":{"mla":"Ojavee, Sven E., et al. “Genetic Insights into the Age-Specific Biological Mechanisms Governing Human Ovarian Aging.” <i>American Journal of Human Genetics</i>, vol. 110, no. 9, Elsevier, 2023, pp. 1549–63, doi:<a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">10.1016/j.ajhg.2023.07.006</a>.","short":"S.E. Ojavee, L. Darrous, M. Patxot, K. Läll, K. Fischer, R. Mägi, Z. Kutalik, M.R. Robinson, American Journal of Human Genetics 110 (2023) 1549–1563.","ieee":"S. E. Ojavee <i>et al.</i>, “Genetic insights into the age-specific biological mechanisms governing human ovarian aging,” <i>American Journal of Human Genetics</i>, vol. 110, no. 9. Elsevier, pp. 1549–1563, 2023.","chicago":"Ojavee, Sven E., Liza Darrous, Marion Patxot, Kristi Läll, Krista Fischer, Reedik Mägi, Zoltan Kutalik, and Matthew Richard Robinson. “Genetic Insights into the Age-Specific Biological Mechanisms Governing Human Ovarian Aging.” <i>American Journal of Human Genetics</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">https://doi.org/10.1016/j.ajhg.2023.07.006</a>.","ista":"Ojavee SE, Darrous L, Patxot M, Läll K, Fischer K, Mägi R, Kutalik Z, Robinson MR. 2023. Genetic insights into the age-specific biological mechanisms governing human ovarian aging. American Journal of Human Genetics. 110(9), 1549–1563.","apa":"Ojavee, S. E., Darrous, L., Patxot, M., Läll, K., Fischer, K., Mägi, R., … Robinson, M. R. (2023). Genetic insights into the age-specific biological mechanisms governing human ovarian aging. <i>American Journal of Human Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">https://doi.org/10.1016/j.ajhg.2023.07.006</a>","ama":"Ojavee SE, Darrous L, Patxot M, et al. Genetic insights into the age-specific biological mechanisms governing human ovarian aging. <i>American Journal of Human Genetics</i>. 2023;110(9):1549-1563. doi:<a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">10.1016/j.ajhg.2023.07.006</a>"},"article_type":"original","ddc":["570"],"title":"Genetic insights into the age-specific biological mechanisms governing human ovarian aging","abstract":[{"lang":"eng","text":"There is currently little evidence that the genetic basis of human phenotype varies significantly across the lifespan. However, time-to-event phenotypes are understudied and can be thought of as reflecting an underlying hazard, which is unlikely to be constant through life when values take a broad range. Here, we find that 74% of 245 genome-wide significant genetic associations with age at natural menopause (ANM) in the UK Biobank show a form of age-specific effect. Nineteen of these replicated discoveries are identified only by our modeling framework, which determines the time dependency of DNA-variant age-at-onset associations without a significant multiple-testing burden. Across the range of early to late menopause, we find evidence for significantly different underlying biological pathways, changes in the signs of genetic correlations of ANM to health indicators and outcomes, and differences in inferred causal relationships. We find that DNA damage response processes only act to shape ovarian reserve and depletion for women of early ANM. Genetically mediated delays in ANM were associated with increased relative risk of breast cancer and leiomyoma at all ages and with high cholesterol and heart failure for late-ANM women. These findings suggest that a better understanding of the age dependency of genetic risk factor relationships among health indicators and outcomes is achievable through appropriate statistical modeling of large-scale biobank data."}],"publication":"American Journal of Human Genetics","publication_status":"published","status":"public","date_updated":"2025-09-09T12:51:20Z","day":"07","oa_version":"Published Version","date_published":"2023-09-07T00:00:00Z","article_processing_charge":"Yes (via OA deal)"},{"pmid":1,"citation":{"apa":"Gamper, J., Kluibenschedl, F., Weiss, A. K. H., &#38; Hofer, T. S. (2023). Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. <i>Journal of Physical Chemistry Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">https://doi.org/10.1021/acs.jpclett.3c01707</a>","ama":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. <i>Journal of Physical Chemistry Letters</i>. 2023;14(33):7395-7403. doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">10.1021/acs.jpclett.3c01707</a>","mla":"Gamper, Jakob, et al. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” <i>Journal of Physical Chemistry Letters</i>, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403, doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">10.1021/acs.jpclett.3c01707</a>.","short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403.","ieee":"J. Gamper, F. Kluibenschedl, A. K. H. Weiss, and T. S. Hofer, “Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems,” <i>Journal of Physical Chemistry Letters</i>, vol. 14, no. 33. American Chemical Society, pp. 7395–7403, 2023.","chicago":"Gamper, Jakob, Florian Kluibenschedl, Alexander K.H. Weiss, and Thomas S. Hofer. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” <i>Journal of Physical Chemistry Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">https://doi.org/10.1021/acs.jpclett.3c01707</a>.","ista":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. 2023. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. 14(33), 7395–7403."},"file":[{"date_created":"2023-09-06T07:32:39Z","content_type":"application/pdf","creator":"dernst","file_id":"14272","checksum":"637454e2b3a357498d8d622d241c4bf6","file_name":"2023_JourPhysChemistry_Gamper.pdf","date_updated":"2023-09-06T07:32:39Z","file_size":4986859,"access_level":"open_access","success":1,"relation":"main_file"}],"article_type":"original","publication_identifier":{"eissn":["1948-7185"]},"intvolume":"        14","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"publisher":"American Chemical Society","volume":14,"page":"7395-7403","month":"08","type":"journal_article","external_id":{"pmid":["37566743"],"isi":["001048165800001"]},"quality_controlled":"1","publication_status":"published","status":"public","publication":"Journal of Physical Chemistry Letters","article_processing_charge":"Yes (in subscription journal)","date_published":"2023-08-11T00:00:00Z","oa_version":"Published Version","date_updated":"2023-09-06T11:04:31Z","day":"11","title":"Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems","ddc":["530","540"],"abstract":[{"lang":"eng","text":"In this work, a generalized, adapted Numerov implementation capable of determining band structures of periodic quantum systems is outlined. Based on the input potential, the presented approach numerically solves the Schrödinger equation in position space at each momentum space point. Thus, in addition to the band structure, the method inherently provides information about the state functions and probability densities in position space at each momentum space point considered. The generalized, adapted Numerov framework provided reliable estimates for a variety of increasingly complex test suites in one, two, and three dimensions. The accuracy of the proposed methodology was benchmarked against results obtained for the analytically solvable Kronig-Penney model. Furthermore, the presented numerical solver was applied to a model potential representing a 2D optical lattice being a challenging application relevant, for example, in the field of quantum computing."}],"scopus_import":"1","issue":"33","acknowledgement":"Financial supports for this work via a PhD scholarship for J. Gamper issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike Tanzer) are gratefully acknowledged. The computational results presented have been achieved (in part) using the HPC infrastructure of the University of Innsbruck.","doi":"10.1021/acs.jpclett.3c01707","has_accepted_license":"1","_id":"14261","date_created":"2023-09-03T22:01:16Z","department":[{"_id":"GradSch"}],"author":[{"last_name":"Gamper","full_name":"Gamper, Jakob","first_name":"Jakob"},{"first_name":"Florian","full_name":"Kluibenschedl, Florian","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","last_name":"Kluibenschedl"},{"last_name":"Weiss","full_name":"Weiss, Alexander K.H.","first_name":"Alexander K.H."},{"last_name":"Hofer","full_name":"Hofer, Thomas S.","first_name":"Thomas S."}],"year":"2023","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"file_date_updated":"2023-09-06T07:32:39Z","language":[{"iso":"eng"}]},{"author":[{"full_name":"Boocock, Daniel R","last_name":"Boocock","id":"453AF628-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1585-2631","first_name":"Daniel R"},{"first_name":"Tsuyoshi","full_name":"Hirashima, Tsuyoshi","last_name":"Hirashima"},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B"}],"date_created":"2023-09-06T08:30:59Z","department":[{"_id":"EdHa"}],"acknowledgement":"We thank all members of the Hannezo group for discussions and suggestions, as well as Sound Wai Phow for technical assistance. This work received funding from the European Research Council under the EU Horizon 2020 research and innovation program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and the Ministry of Education under the Research Centres of Excellence program through the MBI at NUS.","issue":"1","_id":"14277","has_accepted_license":"1","doi":"10.1103/prxlife.1.013001","corr_author":"1","file_date_updated":"2023-09-15T06:30:50Z","language":[{"iso":"eng"}],"article_number":"013001","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","volume":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"American Physical Society","oa":1,"intvolume":"         1","publication_identifier":{"issn":["2835-8279"]},"quality_controlled":"1","month":"07","type":"journal_article","file":[{"content_type":"application/pdf","date_created":"2023-09-15T06:30:50Z","creator":"dernst","file_id":"14335","file_name":"2023_PRXLife_Boocock.pdf","checksum":"f881d98c89eb9f1aa136d7b781511553","access_level":"open_access","file_size":2559520,"date_updated":"2023-09-15T06:30:50Z","success":1,"relation":"main_file"}],"citation":{"ama":"Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. <i>PRX Life</i>. 2023;1(1). doi:<a href=\"https://doi.org/10.1103/prxlife.1.013001\">10.1103/prxlife.1.013001</a>","apa":"Boocock, D. R., Hirashima, T., &#38; Hannezo, E. B. (2023). Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. <i>PRX Life</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxlife.1.013001\">https://doi.org/10.1103/prxlife.1.013001</a>","ieee":"D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers,” <i>PRX Life</i>, vol. 1, no. 1. American Physical Society, 2023.","chicago":"Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” <i>PRX Life</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/prxlife.1.013001\">https://doi.org/10.1103/prxlife.1.013001</a>.","ista":"Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.","mla":"Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” <i>PRX Life</i>, vol. 1, no. 1, 013001, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/prxlife.1.013001\">10.1103/prxlife.1.013001</a>.","short":"D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023)."},"project":[{"name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288"}],"article_type":"original","ddc":["570"],"title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","ec_funded":1,"abstract":[{"text":"Living tissues are characterized by an intrinsically mechanochemical interplay of active physical forces and complex biochemical signaling pathways. Either feature alone can give rise to complex emergent phenomena, for example, mechanically driven glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion instabilities. An important question is how to quantitatively assess the contribution of these different cues to the large-scale dynamics of biological materials. We address this in Madin-Darby canine kidney (MDCK) monolayers, considering both mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling activity and cellular density as well as a mechanically active tissue rheology via a self-propelled vertex model. We show that the relative strength of active migration forces to mechanochemical couplings controls a transition from a uniform active glass to periodic spatiotemporal waves. We parametrize the model from published experimental data sets on MDCK monolayers and use it to make new predictions on the correlation functions of cellular dynamics and the dynamics of topological defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers are best described by an intermediary parameter region in which both mechanochemical couplings and noisy active propulsion have a strong influence on the dynamics. Finally, we study how tissue rheology and ERK waves produce feedback on one another and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical waves at both the local and global levels.","lang":"eng"}],"status":"public","publication":"PRX Life","publication_status":"published","day":"20","date_updated":"2025-04-14T07:52:27Z","oa_version":"Published Version","date_published":"2023-07-20T00:00:00Z","article_processing_charge":"Yes"},{"department":[{"_id":"EdHa"}],"type":"research_data_reference","date_created":"2023-09-06T08:39:25Z","month":"07","author":[{"first_name":"Mehmet C","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","full_name":"Ucar, Mehmet C"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"publisher":"Zenodo","doi":"10.5281/ZENODO.8133960","has_accepted_license":"1","_id":"14279","citation":{"apa":"Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8133960\">https://doi.org/10.5281/ZENODO.8133960</a>","ama":"Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>","short":"M.C. Ucar, (2023).","mla":"Ucar, Mehmet C. <i>Source Data for the Manuscript “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.”</i> Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>.","ista":"Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>.","chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8133960\">https://doi.org/10.5281/ZENODO.8133960</a>.","ieee":"M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023."},"abstract":[{"lang":"eng","text":"The zip file includes source data used in the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript.\r\nA sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8133960"}],"title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","corr_author":"1","ddc":["570"],"date_published":"2023-07-11T00:00:00Z","article_processing_charge":"No","year":"2023","related_material":{"record":[{"status":"public","id":"14274","relation":"used_in_publication"}]},"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"11","date_updated":"2026-06-18T17:34:48Z","status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","language":[{"iso":"eng"}],"_id":"14281","doi":"10.1126/science.adg7731","issue":"6659","scopus_import":"1","author":[{"first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","full_name":"Praetorius, Florian M"},{"first_name":"Philip J. Y.","last_name":"Leung","full_name":"Leung, Philip J. Y."},{"full_name":"Tessmer, Maxx H.","last_name":"Tessmer","first_name":"Maxx H."},{"first_name":"Adam","last_name":"Broerman","full_name":"Broerman, Adam"},{"full_name":"Demakis, Cullen","last_name":"Demakis","first_name":"Cullen"},{"first_name":"Acacia F.","full_name":"Dishman, Acacia F.","last_name":"Dishman"},{"first_name":"Arvind","last_name":"Pillai","full_name":"Pillai, Arvind"},{"first_name":"Abbas","last_name":"Idris","full_name":"Idris, Abbas"},{"full_name":"Juergens, David","last_name":"Juergens","first_name":"David"},{"last_name":"Dauparas","full_name":"Dauparas, Justas","first_name":"Justas"},{"first_name":"Xinting","full_name":"Li, Xinting","last_name":"Li"},{"first_name":"Paul M.","full_name":"Levine, Paul M.","last_name":"Levine"},{"first_name":"Mila","full_name":"Lamb, Mila","last_name":"Lamb"},{"full_name":"Ballard, Ryanne K.","last_name":"Ballard","first_name":"Ryanne K."},{"first_name":"Stacey R.","last_name":"Gerben","full_name":"Gerben, Stacey R."},{"first_name":"Hannah","last_name":"Nguyen","full_name":"Nguyen, Hannah"},{"first_name":"Alex","full_name":"Kang, Alex","last_name":"Kang"},{"full_name":"Sankaran, Banumathi","last_name":"Sankaran","first_name":"Banumathi"},{"full_name":"Bera, Asim K.","last_name":"Bera","first_name":"Asim K."},{"last_name":"Volkman","full_name":"Volkman, Brian F.","first_name":"Brian F."},{"last_name":"Nivala","full_name":"Nivala, Jeff","first_name":"Jeff"},{"first_name":"Stefan","last_name":"Stoll","full_name":"Stoll, Stefan"},{"first_name":"David","full_name":"Baker, David","last_name":"Baker"}],"date_created":"2023-09-06T12:04:23Z","date_updated":"2023-11-07T12:42:09Z","day":"17","oa_version":"None","date_published":"2023-08-17T00:00:00Z","article_processing_charge":"No","status":"public","publication_status":"published","publication":"Science","abstract":[{"lang":"eng","text":"In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing proteins with two distinct but fully structured conformations is a challenge for protein design as it requires sculpting an energy landscape with two distinct minima. Here we describe the design of “hinge” proteins that populate one designed state in the absence of ligand and a second designed state in the presence of ligand. X-ray crystallography, electron microscopy, double electron-electron resonance spectroscopy, and binding measurements demonstrate that despite the significant structural differences the two states are designed with atomic level accuracy and that the conformational and binding equilibria are closely coupled."}],"title":"Design of stimulus-responsive two-state hinge proteins","article_type":"original","citation":{"apa":"Praetorius, F. M., Leung, P. J. Y., Tessmer, M. H., Broerman, A., Demakis, C., Dishman, A. F., … Baker, D. (2023). Design of stimulus-responsive two-state hinge proteins. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adg7731\">https://doi.org/10.1126/science.adg7731</a>","ama":"Praetorius FM, Leung PJY, Tessmer MH, et al. Design of stimulus-responsive two-state hinge proteins. <i>Science</i>. 2023;381(6659):754-760. doi:<a href=\"https://doi.org/10.1126/science.adg7731\">10.1126/science.adg7731</a>","mla":"Praetorius, Florian M., et al. “Design of Stimulus-Responsive Two-State Hinge Proteins.” <i>Science</i>, vol. 381, no. 6659, American Association for the Advancement of Science, 2023, pp. 754–60, doi:<a href=\"https://doi.org/10.1126/science.adg7731\">10.1126/science.adg7731</a>.","short":"F.M. Praetorius, P.J.Y. Leung, M.H. Tessmer, A. Broerman, C. Demakis, A.F. Dishman, A. Pillai, A. Idris, D. Juergens, J. Dauparas, X. Li, P.M. Levine, M. Lamb, R.K. Ballard, S.R. Gerben, H. Nguyen, A. Kang, B. Sankaran, A.K. Bera, B.F. Volkman, J. Nivala, S. Stoll, D. Baker, Science 381 (2023) 754–760.","ieee":"F. M. Praetorius <i>et al.</i>, “Design of stimulus-responsive two-state hinge proteins,” <i>Science</i>, vol. 381, no. 6659. American Association for the Advancement of Science, pp. 754–760, 2023.","ista":"Praetorius FM, Leung PJY, Tessmer MH, Broerman A, Demakis C, Dishman AF, Pillai A, Idris A, Juergens D, Dauparas J, Li X, Levine PM, Lamb M, Ballard RK, Gerben SR, Nguyen H, Kang A, Sankaran B, Bera AK, Volkman BF, Nivala J, Stoll S, Baker D. 2023. Design of stimulus-responsive two-state hinge proteins. Science. 381(6659), 754–760.","chicago":"Praetorius, Florian M, Philip J. Y. Leung, Maxx H. Tessmer, Adam Broerman, Cullen Demakis, Acacia F. Dishman, Arvind Pillai, et al. “Design of Stimulus-Responsive Two-State Hinge Proteins.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adg7731\">https://doi.org/10.1126/science.adg7731</a>."},"pmid":1,"extern":"1","quality_controlled":"1","external_id":{"pmid":["37590357"]},"month":"08","type":"journal_article","page":"754-760","publisher":"American Association for the Advancement of Science","volume":381,"intvolume":"       381","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]}},{"citation":{"short":"N.I. Edman, R.L. Redler, A. Phal, T. Schlichthaerle, S.R. Srivatsan, A. Etemadi, S. An, A. Favor, D. Ehnes, Z. Li, F.M. Praetorius, M. Gordon, W. Yang, B. Coventry, D.R. Hicks, L. Cao, N. Bethel, P. Heine, A.N. Murray, S. Gerben, L. Carter, M. Miranda, B. Negahdari, S. Lee, C. Trapnell, L. Stewart, D.C. Ekiert, J. Schlessinger, J. Shendure, G. Bhabha, H. Ruohola-Baker, D. Baker, BioRxiv (n.d.).","mla":"Edman, Natasha I., et al. “Modulation of FGF Pathway Signaling and Vascular Differentiation Using Designed Oligomeric Assemblies.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2023.03.14.532666\">10.1101/2023.03.14.532666</a>.","chicago":"Edman, Natasha I, Rachel L Redler, Ashish Phal, Thomas Schlichthaerle, Sanjay R Srivatsan, Ali Etemadi, Seong An, et al. “Modulation of FGF Pathway Signaling and Vascular Differentiation Using Designed Oligomeric Assemblies.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2023.03.14.532666\">https://doi.org/10.1101/2023.03.14.532666</a>.","ista":"Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An S, Favor A, Ehnes D, Li Z, Praetorius FM, Gordon M, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray AN, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. bioRxiv, <a href=\"https://doi.org/10.1101/2023.03.14.532666\">10.1101/2023.03.14.532666</a>.","ieee":"N. I. Edman <i>et al.</i>, “Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies,” <i>bioRxiv</i>. .","apa":"Edman, N. I., Redler, R. L., Phal, A., Schlichthaerle, T., Srivatsan, S. R., Etemadi, A., … Baker, D. (n.d.). Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2023.03.14.532666\">https://doi.org/10.1101/2023.03.14.532666</a>","ama":"Edman NI, Redler RL, Phal A, et al. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2023.03.14.532666\">10.1101/2023.03.14.532666</a>"},"doi":"10.1101/2023.03.14.532666","_id":"14294","oa":1,"month":"03","date_created":"2023-09-06T12:31:49Z","type":"preprint","extern":"1","author":[{"first_name":"Natasha I","last_name":"Edman","full_name":"Edman, Natasha I"},{"first_name":"Rachel L","last_name":"Redler","full_name":"Redler, Rachel L"},{"last_name":"Phal","full_name":"Phal, Ashish","first_name":"Ashish"},{"last_name":"Schlichthaerle","full_name":"Schlichthaerle, Thomas","first_name":"Thomas"},{"full_name":"Srivatsan, Sanjay R","last_name":"Srivatsan","first_name":"Sanjay R"},{"full_name":"Etemadi, Ali","last_name":"Etemadi","first_name":"Ali"},{"full_name":"An, Seong","last_name":"An","first_name":"Seong"},{"first_name":"Andrew","last_name":"Favor","full_name":"Favor, Andrew"},{"full_name":"Ehnes, Devon","last_name":"Ehnes","first_name":"Devon"},{"first_name":"Zhe","last_name":"Li","full_name":"Li, Zhe"},{"first_name":"Florian M","full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius"},{"first_name":"Max","full_name":"Gordon, Max","last_name":"Gordon"},{"first_name":"Wei","last_name":"Yang","full_name":"Yang, Wei"},{"first_name":"Brian","full_name":"Coventry, Brian","last_name":"Coventry"},{"last_name":"Hicks","full_name":"Hicks, Derrick R","first_name":"Derrick R"},{"first_name":"Longxing","last_name":"Cao","full_name":"Cao, Longxing"},{"last_name":"Bethel","full_name":"Bethel, Neville","first_name":"Neville"},{"first_name":"Piper","full_name":"Heine, Piper","last_name":"Heine"},{"first_name":"Analisa N","full_name":"Murray, Analisa N","last_name":"Murray"},{"first_name":"Stacey","full_name":"Gerben, Stacey","last_name":"Gerben"},{"first_name":"Lauren","full_name":"Carter, Lauren","last_name":"Carter"},{"first_name":"Marcos","full_name":"Miranda, Marcos","last_name":"Miranda"},{"first_name":"Babak","last_name":"Negahdari","full_name":"Negahdari, Babak"},{"first_name":"Sangwon","full_name":"Lee, Sangwon","last_name":"Lee"},{"full_name":"Trapnell, Cole","last_name":"Trapnell","first_name":"Cole"},{"first_name":"Lance","full_name":"Stewart, Lance","last_name":"Stewart"},{"last_name":"Ekiert","full_name":"Ekiert, Damian C","first_name":"Damian C"},{"full_name":"Schlessinger, Joseph","last_name":"Schlessinger","first_name":"Joseph"},{"full_name":"Shendure, Jay","last_name":"Shendure","first_name":"Jay"},{"first_name":"Gira","full_name":"Bhabha, Gira","last_name":"Bhabha"},{"full_name":"Ruohola-Baker, Hannele","last_name":"Ruohola-Baker","first_name":"Hannele"},{"first_name":"David","last_name":"Baker","full_name":"Baker, David"}],"publication_status":"submitted","status":"public","publication":"bioRxiv","year":"2023","article_processing_charge":"No","date_published":"2023-03-15T00:00:00Z","date_updated":"2023-11-07T12:21:58Z","day":"15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","title":"Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.03.14.532666"}],"abstract":[{"lang":"eng","text":"Growth factors and cytokines signal by binding to the extracellular domains of their receptors and drive association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affects signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo designed fibroblast growth-factor receptor (FGFR) binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation. The high specificity of the designed agonists reveal distinct roles for two FGFR splice variants in driving endothelial and mesenchymal cell fates during early vascular development. The ability to incorporate receptor binding domains and repeat extensions in a modular fashion makes our designed scaffolds broadly useful for probing and manipulating cellular signaling pathways."}]},{"file_date_updated":"2023-11-02T17:03:20Z","corr_author":"1","language":[{"iso":"eng"}],"year":"2023","isi":1,"article_number":"102443","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"JiFr"}],"date_created":"2023-09-10T22:01:11Z","author":[{"first_name":"Lukas","full_name":"Fiedler, Lukas","last_name":"Fiedler","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"scopus_import":"1","acknowledgement":"The opening quote is not intended to reflect any political views of the authors. The authors by no means endorse the rhetoric of Donald Rumsfeld or the 2003 invasion of Iraq by the United States. Nevertheless, Rumsfeld's quote led to both public and academic debates on the concept of known and unknown unknowns, which can be applied to the recent unexpected developments in the auxin signaling field. We thank Linlin Qi and Huihuang Chen for their suggestions on figure presentation and inspiring discussions of TIR1/AFB signaling. Finally, we thank Aroosa Hussain for discussion of Greek mythology.","issue":"10","doi":"10.1016/j.pbi.2023.102443","has_accepted_license":"1","_id":"14313","ddc":["580"],"title":"Rapid auxin signaling: Unknowns old and new","abstract":[{"lang":"eng","text":"To respond to auxin, the chief orchestrator of their multicellularity, plants evolved multiple receptor systems and signal transduction cascades. Despite decades of research, however, we are still lacking a satisfactory synthesis of various auxin signaling mechanisms. The chief discrepancy and historical controversy of the field is that of rapid and slow auxin effects on plant physiology and development. How is it possible that ions begin to trickle across the plasma membrane as soon as auxin enters the cell, even though the best-characterized transcriptional auxin pathway can take effect only after tens of minutes? Recently, unexpected progress has been made in understanding this and other unknowns of auxin signaling. We provide a perspective on these exciting developments and concepts whose general applicability might have ramifications beyond auxin signaling."}],"publication":"Current Opinion in Plant Biology","status":"public","publication_status":"published","article_processing_charge":"No","date_published":"2023-10-01T00:00:00Z","date_updated":"2025-09-09T12:54:16Z","day":"01","oa_version":"Submitted Version","intvolume":"        75","publication_identifier":{"issn":["1369-5266"]},"publisher":"Elsevier","volume":75,"oa":1,"month":"10","external_id":{"isi":["001080095300001"],"pmid":["37666097"]},"type":"journal_article","quality_controlled":"1","file":[{"success":1,"relation":"main_file","date_updated":"2023-11-02T17:03:20Z","access_level":"open_access","file_size":737872,"file_id":"14482","file_name":"Fiedler CurrOpinOlantBiol 2023_revised.pdf","checksum":"1c476c3414d2dfb0c85db0cb6cfd8a28","date_created":"2023-11-02T17:03:20Z","content_type":"application/pdf","creator":"amally"}],"citation":{"ama":"Fiedler L, Friml J. Rapid auxin signaling: Unknowns old and new. <i>Current Opinion in Plant Biology</i>. 2023;75(10). doi:<a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">10.1016/j.pbi.2023.102443</a>","apa":"Fiedler, L., &#38; Friml, J. (2023). Rapid auxin signaling: Unknowns old and new. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">https://doi.org/10.1016/j.pbi.2023.102443</a>","ieee":"L. Fiedler and J. Friml, “Rapid auxin signaling: Unknowns old and new,” <i>Current Opinion in Plant Biology</i>, vol. 75, no. 10. Elsevier, 2023.","chicago":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">https://doi.org/10.1016/j.pbi.2023.102443</a>.","ista":"Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 75(10), 102443.","mla":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” <i>Current Opinion in Plant Biology</i>, vol. 75, no. 10, 102443, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">10.1016/j.pbi.2023.102443</a>.","short":"L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (2023)."},"pmid":1,"article_type":"review"},{"scopus_import":"1","acknowledgement":"We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS (grant 607616).","issue":"9","has_accepted_license":"1","doi":"10.1016/j.celrep.2023.113015","_id":"14314","department":[{"_id":"JoCs"}],"date_created":"2023-09-10T22:01:11Z","author":[{"id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin","full_name":"Nardin, Michele","first_name":"Michele","orcid":"0000-0001-8849-6570"},{"first_name":"Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","last_name":"Käfer","full_name":"Käfer, Karola"},{"full_name":"Stella, Federico","last_name":"Stella","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9439-3148","first_name":"Federico"},{"orcid":"0000-0002-5193-4036","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari"}],"year":"2023","isi":1,"article_number":"113015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2023-09-15T07:12:46Z","corr_author":"1","language":[{"iso":"eng"}],"file":[{"checksum":"ca77a304fb813c292550b8604b0fb41d","file_name":"2023_CellPress_Nardin.pdf","file_id":"14337","creator":"dernst","content_type":"application/pdf","date_created":"2023-09-15T07:12:46Z","relation":"main_file","success":1,"access_level":"open_access","file_size":4879455,"date_updated":"2023-09-15T07:12:46Z"}],"citation":{"ieee":"M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions,” <i>Cell Reports</i>, vol. 42, no. 9. Elsevier, 2023.","chicago":"Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” <i>Cell Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">https://doi.org/10.1016/j.celrep.2023.113015</a>.","ista":"Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9), 113015.","mla":"Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” <i>Cell Reports</i>, vol. 42, no. 9, 113015, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">10.1016/j.celrep.2023.113015</a>.","short":"M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023).","ama":"Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. <i>Cell Reports</i>. 2023;42(9). doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">10.1016/j.celrep.2023.113015</a>","apa":"Nardin, M., Käfer, K., Stella, F., &#38; Csicsvari, J. L. (2023). Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">https://doi.org/10.1016/j.celrep.2023.113015</a>"},"pmid":1,"project":[{"name":"inter-and intracellular signalling in schizophrenia","call_identifier":"FP7","grant_number":"607616","_id":"257BBB4C-B435-11E9-9278-68D0E5697425"}],"article_type":"original","intvolume":"        42","publication_identifier":{"eissn":["2211-1247"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Elsevier","oa":1,"volume":42,"month":"09","external_id":{"pmid":["37632747"],"isi":["001068779200001"]},"type":"journal_article","quality_controlled":"1","publication_status":"published","status":"public","publication":"Cell Reports","article_processing_charge":"Yes","date_published":"2023-09-26T00:00:00Z","date_updated":"2025-09-09T12:53:32Z","day":"26","oa_version":"Published Version","ddc":["570"],"title":"Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions","abstract":[{"lang":"eng","text":"The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations."}],"ec_funded":1},{"file":[{"date_updated":"2023-09-15T06:59:10Z","access_level":"open_access","file_size":3703097,"relation":"main_file","success":1,"creator":"dernst","content_type":"application/pdf","date_created":"2023-09-15T06:59:10Z","checksum":"db24bf3d595507387b48d3799c33e289","file_name":"2023_eLife_Cho.pdf","file_id":"14336"}],"citation":{"ama":"Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. <i>eLife</i>. 2023;12. doi:<a href=\"https://doi.org/10.7554/eLife.89066\">10.7554/eLife.89066</a>","apa":"Cho, U. H., &#38; Hetzer, M. (2023). Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.89066\">https://doi.org/10.7554/eLife.89066</a>","ieee":"U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2023.","chicago":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” <i>ELife</i>. eLife Sciences Publications, 2023. <a href=\"https://doi.org/10.7554/eLife.89066\">https://doi.org/10.7554/eLife.89066</a>.","ista":"Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.","mla":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” <i>ELife</i>, vol. 12, RP89066, eLife Sciences Publications, 2023, doi:<a href=\"https://doi.org/10.7554/eLife.89066\">10.7554/eLife.89066</a>.","short":"U.H. Cho, M. Hetzer, ELife 12 (2023)."},"pmid":1,"article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":12,"oa":1,"publisher":"eLife Sciences Publications","intvolume":"        12","publication_identifier":{"eissn":["2050-084X"]},"quality_controlled":"1","month":"09","type":"journal_article","external_id":{"pmid":["37665327"]},"publication_status":"published","publication":"eLife","status":"public","date_updated":"2024-10-09T21:06:57Z","day":"04","oa_version":"Published Version","date_published":"2023-09-04T00:00:00Z","article_processing_charge":"Yes","ddc":["570"],"title":"Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress","abstract":[{"lang":"eng","text":"During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels."}],"acknowledgement":"We thank the members of the Hetzer laboratory, Tony Hunter (Salk), Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital) for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin (Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH), and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC). This work was also supported by the Mass Spectrometry Core of the Salk Institute with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine. We thank Jolene Diedrich and Antonio Pinto for technical support.","scopus_import":"1","_id":"14315","has_accepted_license":"1","doi":"10.7554/eLife.89066","author":[{"last_name":"Cho","full_name":"Cho, Ukrae H.","first_name":"Ukrae H."},{"full_name":"Hetzer, Martin W","last_name":"Hetzer","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","first_name":"Martin W"}],"department":[{"_id":"MaHe"}],"date_created":"2023-09-10T22:01:11Z","article_number":"RP89066","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","corr_author":"1","file_date_updated":"2023-09-15T06:59:10Z","language":[{"iso":"eng"}]},{"author":[{"first_name":"Makoto","full_name":"Nagano, Makoto","last_name":"Nagano"},{"first_name":"Kaito","last_name":"Aoshima","full_name":"Aoshima, Kaito"},{"first_name":"Hiroki","last_name":"Shimamura","full_name":"Shimamura, Hiroki"},{"first_name":"Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E"},{"full_name":"Toshima, Junko Y.","last_name":"Toshima","first_name":"Junko Y."},{"last_name":"Toshima","full_name":"Toshima, Jiro","first_name":"Jiro"}],"department":[{"_id":"DaSi"}],"date_created":"2023-09-10T22:01:12Z","_id":"14316","doi":"10.1242/jcs.261448","issue":"17","scopus_import":"1","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.03.27.534325"}],"article_number":"jcs261448","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2023","quality_controlled":"1","type":"journal_article","month":"09","external_id":{"pmid":["37539494"],"isi":["001112832300005"]},"oa":1,"volume":136,"publisher":"The Company of Biologists","intvolume":"       136","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"article_type":"original","pmid":1,"citation":{"ama":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. <i>Journal of Cell Science</i>. 2023;136(17). doi:<a href=\"https://doi.org/10.1242/jcs.261448\">10.1242/jcs.261448</a>","apa":"Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., &#38; Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261448\">https://doi.org/10.1242/jcs.261448</a>","ista":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. 136(17), jcs261448.","chicago":"Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.261448\">https://doi.org/10.1242/jcs.261448</a>.","ieee":"M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J. Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway,” <i>Journal of Cell Science</i>, vol. 136, no. 17. The Company of Biologists, 2023.","short":"M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Science 136 (2023).","mla":"Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” <i>Journal of Cell Science</i>, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.261448\">10.1242/jcs.261448</a>."},"abstract":[{"text":"Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport. In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted to generate distinct transport vesicles at the trans-Golgi network (TGN), and the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories for these adaptors. Recently, we showed that vesicle transport from the TGN is crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However, these observations were incompatible with previous studies showing that these adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall mechanism responsible for regulation of Vps21p activity remains ambiguous. Here, we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and Ypt32p were found to have partially overlapping functions for recruitment of AP-1 and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors for Vps21p activation in the TGN–endosome trafficking pathway.","lang":"eng"}],"title":"Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway","date_updated":"2025-09-09T12:56:46Z","day":"01","oa_version":"Preprint","date_published":"2023-09-01T00:00:00Z","article_processing_charge":"No","publication_status":"published","publication":"Journal of Cell Science","status":"public"},{"file":[{"content_type":"application/pdf","date_created":"2023-09-20T08:46:43Z","creator":"dernst","file_id":"14349","file_name":"2023_LNCS_Akshay.pdf","checksum":"f143c8eedf609f20f2aad2eeb496d53f","file_size":531745,"access_level":"open_access","date_updated":"2023-09-20T08:46:43Z","success":1,"relation":"main_file"}],"citation":{"mla":"Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” <i>International Conference on Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 86–112, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>.","short":"S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112.","ieee":"S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution transformers: Affine invariant synthesis for safety objectives,” in <i>International Conference on Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 86–112.","chicago":"Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” In <i>International Conference on Computer Aided Verification</i>, 13966:86–112. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>.","ista":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 86–112.","apa":"Akshay, S., Chatterjee, K., Meggendorfer, T., &#38; Zikelic, D. (2023). MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In <i>International Conference on Computer Aided Verification</i> (Vol. 13966, pp. 86–112). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>","ama":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In: <i>International Conference on Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:86-112. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>"},"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"publisher":"Springer Nature","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":13966,"oa":1,"conference":{"location":"Paris, France","name":"CAV: Computer Aided Verification","start_date":"2023-07-17","end_date":"2023-07-22"},"intvolume":"     13966","publication_identifier":{"isbn":["9783031377082"],"eissn":["1611-3349"],"issn":["0302-9743"]},"quality_controlled":"1","month":"07","external_id":{"isi":["001310805600005"]},"type":"conference","page":"86-112","status":"public","publication_status":"published","publication":"International Conference on Computer Aided Verification","day":"17","date_updated":"2025-09-09T12:56:00Z","alternative_title":["LNCS"],"oa_version":"Published Version","date_published":"2023-07-17T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","ddc":["000"],"title":"MDPs as distribution transformers: Affine invariant synthesis for safety objectives","ec_funded":1,"abstract":[{"lang":"eng","text":"Markov decision processes can be viewed as transformers of probability distributions. While this view is useful from a practical standpoint to reason about trajectories of distributions, basic reachability and safety problems are known to be computationally intractable (i.e., Skolem-hard) to solve in such models. Further, we show that even for simple examples of MDPs, strategies for safety objectives over distributions can require infinite memory and randomization.\r\nIn light of this, we present a novel overapproximation approach to synthesize strategies in an MDP, such that a safety objective over the distributions is met. More precisely, we develop a new framework for template-based synthesis of certificates as affine distributional and inductive invariants for safety objectives in MDPs. We provide two algorithms within this framework. One can only synthesize memoryless strategies, but has relative completeness guarantees, while the other can synthesize general strategies. The runtime complexity of both algorithms is in PSPACE. We implement these algorithms and show that they can solve several non-trivial examples."}],"acknowledgement":"This work was supported in part by the ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 as well as DST/CEFIPRA/INRIA project EQuaVE and SERB Matrices grant MTR/2018/00074.","scopus_import":"1","_id":"14317","doi":"10.1007/978-3-031-37709-9_5","has_accepted_license":"1","author":[{"full_name":"Akshay, S.","last_name":"Akshay","first_name":"S."},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Meggendorfer","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias","first_name":"Tobias","orcid":"0000-0002-1712-2165"},{"orcid":"0000-0002-4681-1699","first_name":"Dorde","full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic"}],"department":[{"_id":"KrCh"}],"date_created":"2023-09-10T22:01:12Z","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2023","file_date_updated":"2023-09-20T08:46:43Z","language":[{"iso":"eng"}]},{"date_created":"2023-09-10T22:01:12Z","department":[{"_id":"KrCh"}],"author":[{"first_name":"Yican","full_name":"Sun, Yican","last_name":"Sun"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar"}],"doi":"10.1007/978-3-031-37709-9_2","has_accepted_license":"1","_id":"14318","scopus_import":"1","acknowledgement":"We thank Prof. Bican Xia for valuable information on the exponential theory of reals. The work is partially supported by the National Natural Science Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt), the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272.","language":[{"iso":"eng"}],"file_date_updated":"2023-09-20T08:24:47Z","related_material":{"link":[{"relation":"software","url":"https://github.com/boyvolcano/PRR"}]},"year":"2023","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001310805600002"]},"month":"07","type":"conference","page":"16-39","quality_controlled":"1","intvolume":"     13966","conference":{"end_date":"2023-07-22","start_date":"2023-07-17","name":"CAV: Computer Aided Verification","location":"Paris, France"},"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031377082"],"issn":["0302-9743"]},"volume":13966,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Springer Nature","oa":1,"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020"}],"file":[{"date_updated":"2023-09-20T08:24:47Z","access_level":"open_access","file_size":624647,"relation":"main_file","success":1,"creator":"dernst","content_type":"application/pdf","date_created":"2023-09-20T08:24:47Z","file_name":"2023_LNCS_Sun.pdf","checksum":"42917e086f8c7699f3bccf84f74fe000","file_id":"14348"}],"citation":{"apa":"Sun, Y., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2023). Automated tail bound analysis for probabilistic recurrence relations. In <i>Computer Aided Verification</i> (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">https://doi.org/10.1007/978-3-031-37709-9_2</a>","ama":"Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic recurrence relations. In: <i>Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:16-39. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">10.1007/978-3-031-37709-9_2</a>","short":"Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification, Springer Nature, 2023, pp. 16–39.","mla":"Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” <i>Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 16–39, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">10.1007/978-3-031-37709-9_2</a>.","ista":"Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 16–39.","chicago":"Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In <i>Computer Aided Verification</i>, 13966:16–39. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">https://doi.org/10.1007/978-3-031-37709-9_2</a>.","ieee":"Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound analysis for probabilistic recurrence relations,” in <i>Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 16–39."},"abstract":[{"lang":"eng","text":"Probabilistic recurrence relations (PRRs) are a standard formalism for describing the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem, the classical and most well-known approach is the cookbook method by Karp (JACM 1994), while other approaches are mostly limited to deriving tail bounds of specific PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing time and random passed sizes observe discrete or (piecewise) uniform distribution and whose recursive call is either a single procedure call or a divide-and-conquer. We first establish a theoretical approach via Markov’s inequality, and then instantiate the theoretical approach with a template-based algorithmic approach via a refined treatment of exponentiation. Experimental evaluation shows that our algorithmic approach is capable of deriving tail bounds that are (i) asymptotically tighter than Karp’s method, (ii) match the best-known manually-derived asymptotic tail bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor) than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover, our algorithmic approach handles all examples (including realistic PRRs such as QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing that our approach is efficient in practice."}],"ec_funded":1,"ddc":["000"],"title":"Automated tail bound analysis for probabilistic recurrence relations","date_published":"2023-07-17T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","day":"17","alternative_title":["LNCS"],"date_updated":"2025-09-09T12:55:28Z","oa_version":"Published Version","publication_status":"published","status":"public","publication":"Computer Aided Verification"},{"year":"2023","license":"https://creativecommons.org/licenses/by-nd/4.0/","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"P3.10","isi":1,"file_date_updated":"2023-09-15T08:02:09Z","language":[{"iso":"eng"}],"scopus_import":"1","issue":"3","acknowledgement":"Anastos has received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Sk lodowska-Curie grant agreement No 101034413.Fabian’s research is supported by the Deutsche Forschungsgemeinschaft (DFG, GermanResearch Foundation) Graduiertenkolleg “Facets of Complexity” (GRK 2434).","doi":"10.37236/11714","has_accepted_license":"1","_id":"14319","department":[{"_id":"MaKw"}],"date_created":"2023-09-10T22:01:12Z","author":[{"first_name":"Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","last_name":"Anastos","full_name":"Anastos, Michael"},{"full_name":"Fabian, David","last_name":"Fabian","first_name":"David"},{"last_name":"Müyesser","full_name":"Müyesser, Alp","first_name":"Alp"},{"first_name":"Tibor","last_name":"Szabó","full_name":"Szabó, Tibor"}],"status":"public","publication":"Electronic Journal of Combinatorics","publication_status":"published","date_published":"2023-07-28T00:00:00Z","article_processing_charge":"Yes","oa_version":"Published Version","date_updated":"2025-09-09T12:54:51Z","day":"28","title":"Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets","ddc":["510"],"abstract":[{"lang":"eng","text":"We study multigraphs whose edge-sets are the union of three perfect matchings, M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6 n - 2, we show there exists a matching M of G with jM \\ Mij = ai for each i 2 f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture however that if G is bipartite, the same result holds with n - 2 replaced by n - 1. We give a construction that shows such a result would be tight. We\r\nalso make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour\r\nmultiplicities."}],"arxiv":1,"ec_funded":1,"citation":{"ieee":"M. Anastos, D. Fabian, A. Müyesser, and T. Szabó, “Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets,” <i>Electronic Journal of Combinatorics</i>, vol. 30, no. 3. Electronic Journal of Combinatorics, 2023.","ista":"Anastos M, Fabian D, Müyesser A, Szabó T. 2023. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. 30(3), P3.10.","chicago":"Anastos, Michael, David Fabian, Alp Müyesser, and Tibor Szabó. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics, 2023. <a href=\"https://doi.org/10.37236/11714\">https://doi.org/10.37236/11714</a>.","mla":"Anastos, Michael, et al. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” <i>Electronic Journal of Combinatorics</i>, vol. 30, no. 3, P3.10, Electronic Journal of Combinatorics, 2023, doi:<a href=\"https://doi.org/10.37236/11714\">10.37236/11714</a>.","short":"M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics 30 (2023).","ama":"Anastos M, Fabian D, Müyesser A, Szabó T. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. <i>Electronic Journal of Combinatorics</i>. 2023;30(3). doi:<a href=\"https://doi.org/10.37236/11714\">10.37236/11714</a>","apa":"Anastos, M., Fabian, D., Müyesser, A., &#38; Szabó, T. (2023). Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/11714\">https://doi.org/10.37236/11714</a>"},"file":[{"date_updated":"2023-09-15T08:02:09Z","access_level":"open_access","file_size":247917,"relation":"main_file","success":1,"creator":"dernst","content_type":"application/pdf","date_created":"2023-09-15T08:02:09Z","checksum":"52c46c8cb329f9aaee9ade01525f317b","file_name":"2023_elecJournCombinatorics_Anastos.pdf","file_id":"14338"}],"article_type":"original","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"publication_identifier":{"eissn":["1077-8926"]},"intvolume":"        30","tmp":{"image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"volume":30,"publisher":"Electronic Journal of Combinatorics","oa":1,"month":"07","external_id":{"isi":["001042382200001"],"arxiv":["2212.03100"]},"type":"journal_article","quality_controlled":"1"},{"abstract":[{"text":"The development of two-dimensional materials has resulted in a diverse range of novel, high-quality compounds with increasing complexity. A key requirement for a comprehensive quantitative theory is the accurate determination of these materials' band structure parameters. However, this task is challenging due to the intricate band structures and the indirect nature of experimental probes. In this work, we introduce a general framework to derive band structure parameters from experimental data using deep neural networks. We applied our method to the penetration field capacitance measurement of trilayer graphene, an effective probe of its density of states. First, we demonstrate that a trained deep network gives accurate predictions for the penetration field capacitance as a function of tight-binding parameters. Next, we use the fast and accurate predictions from the trained network to automatically determine tight-binding parameters directly from experimental data, with extracted parameters being in a good agreement with values in the literature. We conclude by discussing potential applications of our method to other materials and experimental techniques beyond penetration field capacitance.","lang":"eng"}],"arxiv":1,"title":"Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene","oa_version":"Preprint","day":"15","date_updated":"2023-09-20T09:38:24Z","article_processing_charge":"No","date_published":"2023-09-15T00:00:00Z","status":"public","publication":"Physical Review B","publication_status":"published","quality_controlled":"1","month":"09","external_id":{"arxiv":["2210.06310"]},"type":"journal_article","publisher":"American Physical Society","volume":108,"oa":1,"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"intvolume":"       108","article_type":"original","citation":{"apa":"Henderson, P. M., Ghazaryan, A., Zibrov, A. A., Young, A. F., &#38; Serbyn, M. (2023). Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.108.125411\">https://doi.org/10.1103/physrevb.108.125411</a>","ama":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. <i>Physical Review B</i>. 2023;108(12). doi:<a href=\"https://doi.org/10.1103/physrevb.108.125411\">10.1103/physrevb.108.125411</a>","mla":"Henderson, Paul M., et al. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” <i>Physical Review B</i>, vol. 108, no. 12, 125411, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevb.108.125411\">10.1103/physrevb.108.125411</a>.","short":"P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical Review B 108 (2023).","ieee":"P. M. Henderson, A. Ghazaryan, A. A. Zibrov, A. F. Young, and M. Serbyn, “Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene,” <i>Physical Review B</i>, vol. 108, no. 12. American Physical Society, 2023.","ista":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. 2023. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. 108(12), 125411.","chicago":"Henderson, Paul M, Areg Ghazaryan, Alexander A. Zibrov, Andrea F. Young, and Maksym Serbyn. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevb.108.125411\">https://doi.org/10.1103/physrevb.108.125411</a>."},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2210.06310"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"125411","year":"2023","author":[{"full_name":"Henderson, Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425","last_name":"Henderson","orcid":"0000-0002-5198-7445","first_name":"Paul M"},{"orcid":"0000-0001-9666-3543","first_name":"Areg","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander A.","last_name":"Zibrov","full_name":"Zibrov, Alexander A."},{"first_name":"Andrea F.","last_name":"Young","full_name":"Young, Andrea F."},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"MaSe"},{"_id":"ChLa"},{"_id":"MiLe"}],"date_created":"2023-09-12T07:12:12Z","_id":"14320","doi":"10.1103/physrevb.108.125411","issue":"12","acknowledgement":"A.F.Y. acknowledges primary support from the Department of Energy under award DE-SC0020043, and additional support from the Gordon and Betty Moore Foundation under award GBMF9471 for group operations.","scopus_import":"1"},{"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"isi":1,"article_number":"104103","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2023","corr_author":"1","file_date_updated":"2023-09-13T09:34:20Z","language":[{"iso":"eng"}],"acknowledgement":"We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan, and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received funding from the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot.","issue":"10","scopus_import":"1","_id":"14321","doi":"10.1063/5.0165806","has_accepted_license":"1","author":[{"first_name":"Ragheed","full_name":"Al Hyder, Ragheed","last_name":"Al Hyder","id":"d1c405be-ae15-11ed-8510-ccf53278162e"},{"orcid":"0000-0001-6110-2359","first_name":"Alberto","full_name":"Cappellaro, Alberto","last_name":"Cappellaro","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","orcid":"0000-0002-6990-7802"},{"first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","full_name":"Volosniev, Artem"}],"department":[{"_id":"MiLe"}],"date_created":"2023-09-13T09:25:09Z","status":"public","publication_status":"published","publication":"The Journal of Chemical Physics","day":"11","date_updated":"2025-09-09T12:57:42Z","oa_version":"Published Version","date_published":"2023-09-11T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","ddc":["530"],"title":"Achiral dipoles on a ferromagnet can affect its magnetization direction","ec_funded":1,"arxiv":1,"abstract":[{"text":"We demonstrate the possibility of a coupling between the magnetization direction of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate the mechanism of the coupling, we analyze a minimal Stoner model that includes Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet. The proposed mechanism allows us to study magnetic anisotropy of the system with an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can change magnetocrystalline anisotropy of the substrate. Our research aims to motivate further experimental studies of the current-free chirality induced spin selectivity effect involving both enantiomers.","lang":"eng"}],"file":[{"date_updated":"2023-09-13T09:34:20Z","file_size":5749653,"access_level":"open_access","success":1,"relation":"main_file","content_type":"application/pdf","date_created":"2023-09-13T09:34:20Z","creator":"acappell","file_id":"14322","checksum":"507ab65ab29e2c987c94cabad7c5370b","file_name":"104103_1_5.0165806.pdf"}],"citation":{"ama":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet can affect its magnetization direction. <i>The Journal of Chemical Physics</i>. 2023;159(10). doi:<a href=\"https://doi.org/10.1063/5.0165806\">10.1063/5.0165806</a>","apa":"Al Hyder, R., Cappellaro, A., Lemeshko, M., &#38; Volosniev, A. (2023). Achiral dipoles on a ferromagnet can affect its magnetization direction. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0165806\">https://doi.org/10.1063/5.0165806</a>","ieee":"R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles on a ferromagnet can affect its magnetization direction,” <i>The Journal of Chemical Physics</i>, vol. 159, no. 10. AIP Publishing, 2023.","chicago":"Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0165806\">https://doi.org/10.1063/5.0165806</a>.","ista":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. 159(10), 104103.","mla":"Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” <i>The Journal of Chemical Physics</i>, vol. 159, no. 10, 104103, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0165806\">10.1063/5.0165806</a>.","short":"R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical Physics 159 (2023)."},"pmid":1,"project":[{"name":"Non-Equilibrium Field Theory of Molecular Rotations","_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338","grant_number":"101062862"},{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020"}],"article_type":"original","publisher":"AIP Publishing","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"volume":159,"intvolume":"       159","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"quality_controlled":"1","type":"journal_article","external_id":{"pmid":["37694742"],"isi":["001133333600011"],"arxiv":["2306.17592"]},"month":"09"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_updated":"2024-10-14T12:31:20Z","article_number":"2307.09552","day":"18","date_published":"2023-07-18T00:00:00Z","article_processing_charge":"No","year":"2023","publication":"arXiv","status":"public","publication_status":"submitted","abstract":[{"text":"As causal ground truth is incredibly rare, causal discovery algorithms are\r\ncommonly only evaluated on simulated data. This is concerning, given that\r\nsimulations reflect common preconceptions about generating processes regarding\r\nnoise distributions, model classes, and more. In this work, we propose a novel\r\nmethod for falsifying the output of a causal discovery algorithm in the absence\r\nof ground truth. Our key insight is that while statistical learning seeks\r\nstability across subsets of data points, causal learning should seek stability\r\nacross subsets of variables. Motivated by this insight, our method relies on a\r\nnotion of compatibility between causal graphs learned on different subsets of\r\nvariables. We prove that detecting incompatibilities can falsify wrongly\r\ninferred causal relations due to violation of assumptions or errors from finite\r\nsample effects. Although passing such compatibility tests is only a necessary\r\ncriterion for good performance, we argue that it provides strong evidence for\r\nthe causal models whenever compatibility entails strong implications for the\r\njoint distribution. We also demonstrate experimentally that detection of\r\nincompatibilities can aid in causal model selection.","lang":"eng"}],"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2307.09552","open_access":"1"}],"arxiv":1,"title":"Self-compatibility: Evaluating causal discovery without ground truth","_id":"14333","doi":"10.48550/arXiv.2307.09552","citation":{"ieee":"P. M. Faller, L. C. Vankadara, A. A. Mastakouri, F. Locatello, and D. Janzing, “Self-compatibility: Evaluating causal discovery without ground truth,” <i>arXiv</i>. .","ista":"Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility: Evaluating causal discovery without ground truth. arXiv, 2307.09552.","chicago":"Faller, Philipp M., Leena Chennuru Vankadara, Atalanti A. Mastakouri, Francesco Locatello, and Dominik Janzing. “Self-Compatibility: Evaluating Causal Discovery without Ground Truth.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2307.09552\">https://doi.org/10.48550/arXiv.2307.09552</a>.","mla":"Faller, Philipp M., et al. “Self-Compatibility: Evaluating Causal Discovery without Ground Truth.” <i>ArXiv</i>, 2307.09552, doi:<a href=\"https://doi.org/10.48550/arXiv.2307.09552\">10.48550/arXiv.2307.09552</a>.","short":"P.M. Faller, L.C. Vankadara, A.A. Mastakouri, F. Locatello, D. Janzing, ArXiv (n.d.).","ama":"Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility: Evaluating causal discovery without ground truth. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2307.09552\">10.48550/arXiv.2307.09552</a>","apa":"Faller, P. M., Vankadara, L. C., Mastakouri, A. A., Locatello, F., &#38; Janzing, D. (n.d.). Self-compatibility: Evaluating causal discovery without ground truth. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2307.09552\">https://doi.org/10.48550/arXiv.2307.09552</a>"},"author":[{"last_name":"Faller","full_name":"Faller, Philipp M.","first_name":"Philipp M."},{"full_name":"Vankadara, Leena Chennuru","last_name":"Vankadara","first_name":"Leena Chennuru"},{"last_name":"Mastakouri","full_name":"Mastakouri, Atalanti A.","first_name":"Atalanti A."},{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","first_name":"Francesco","orcid":"0000-0002-4850-0683"},{"first_name":"Dominik","last_name":"Janzing","full_name":"Janzing, Dominik"}],"extern":"1","external_id":{"arxiv":["2307.09552"]},"date_created":"2023-09-13T12:44:59Z","department":[{"_id":"FrLo"}],"type":"preprint","month":"07","oa":1},{"ec_funded":1,"abstract":[{"text":"Quantum kinetically constrained models have recently attracted significant attention due to their anomalous dynamics and thermalization. In this work, we introduce a hitherto unexplored family of kinetically constrained models featuring conserved particle number and strong inversion-symmetry breaking due to facilitated hopping. We demonstrate that these models provide a generic example of so-called quantum Hilbert space fragmentation, that is manifested in disconnected sectors in the Hilbert space that are not apparent in the computational basis. Quantum Hilbert space fragmentation leads to an exponential in system size number of eigenstates with exactly zero entanglement entropy across several bipartite cuts. These eigenstates can be probed dynamically using quenches from simple initial product states. In addition, we study the particle spreading under unitary dynamics launched from the domain wall state, and find faster than diffusive dynamics at high particle densities, that crosses over into logarithmically slow relaxation at smaller densities. Using a classically simulable cellular automaton, we reproduce the logarithmic dynamics observed in the quantum case. Our work suggests that particle conserving constrained models with inversion symmetry breaking realize so far unexplored dynamical behavior and invite their further theoretical and experimental studies.","lang":"eng"}],"arxiv":1,"title":"Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models","ddc":["530"],"oa_version":"Published Version","day":"13","date_updated":"2025-04-14T07:52:05Z","article_processing_charge":"No","date_published":"2023-09-13T00:00:00Z","publication":"SciPost Physics","status":"public","publication_status":"published","quality_controlled":"1","month":"09","external_id":{"arxiv":["2210.15607"]},"type":"journal_article","volume":15,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"SciPost Foundation","oa":1,"publication_identifier":{"issn":["2542-4653"]},"intvolume":"        15","article_type":"original","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"citation":{"apa":"Brighi, P., Ljubotina, M., &#38; Serbyn, M. (2023). Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">https://doi.org/10.21468/scipostphys.15.3.093</a>","ama":"Brighi P, Ljubotina M, Serbyn M. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. <i>SciPost Physics</i>. 2023;15(3). doi:<a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">10.21468/scipostphys.15.3.093</a>","mla":"Brighi, Pietro, et al. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” <i>SciPost Physics</i>, vol. 15, no. 3, 093, SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">10.21468/scipostphys.15.3.093</a>.","short":"P. Brighi, M. Ljubotina, M. Serbyn, SciPost Physics 15 (2023).","ieee":"P. Brighi, M. Ljubotina, and M. Serbyn, “Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models,” <i>SciPost Physics</i>, vol. 15, no. 3. SciPost Foundation, 2023.","chicago":"Brighi, Pietro, Marko Ljubotina, and Maksym Serbyn. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” <i>SciPost Physics</i>. SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">https://doi.org/10.21468/scipostphys.15.3.093</a>.","ista":"Brighi P, Ljubotina M, Serbyn M. 2023. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. 15(3), 093."},"file":[{"checksum":"4cef6a8021f6b6c47ab2f2f2b1387ac2","file_name":"2023_SciPostPhysics_Brighi.pdf","file_id":"14350","creator":"dernst","date_created":"2023-09-20T10:46:10Z","content_type":"application/pdf","relation":"main_file","success":1,"date_updated":"2023-09-20T10:46:10Z","access_level":"open_access","file_size":4866506}],"language":[{"iso":"eng"}],"corr_author":"1","file_date_updated":"2023-09-20T10:46:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"093","year":"2023","related_material":{"record":[{"status":"public","id":"12750","relation":"earlier_version"}]},"keyword":["General Physics and Astronomy"],"author":[{"orcid":"0000-0002-7969-2729","first_name":"Pietro","full_name":"Brighi, Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi"},{"orcid":"0000-0003-0038-7068","first_name":"Marko","full_name":"Ljubotina, Marko","last_name":"Ljubotina","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E"},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-09-14T13:08:23Z","department":[{"_id":"MaSe"}],"_id":"14334","doi":"10.21468/scipostphys.15.3.093","has_accepted_license":"1","issue":"3","acknowledgement":"We would like to thank Raimel A. Medina, Hansveer Singh, and Dmitry Abanin for useful\r\ndiscussions.The authors acknowledge support by the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). We acknowledge support by the Erwin Schrödinger International\r\nInstitute for Mathematics and Physics (ESI).","scopus_import":"1"},{"quality_controlled":"1","page":"1500-1513","type":"journal_article","month":"09","external_id":{"isi":["001069238800014"],"pmid":["37666965"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":9,"oa":1,"publisher":"Springer Nature","publication_identifier":{"issn":["2055-0278"]},"intvolume":"         9","article_type":"original","pmid":1,"citation":{"apa":"Roychoudhry, S., Sageman-Furnas, K., Wolverton, C., Grones, P., Tan, S., Molnar, G., … Kepinski, S. (2023). Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-023-01478-x\">https://doi.org/10.1038/s41477-023-01478-x</a>","ama":"Roychoudhry S, Sageman-Furnas K, Wolverton C, et al. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. <i>Nature Plants</i>. 2023;9:1500-1513. doi:<a href=\"https://doi.org/10.1038/s41477-023-01478-x\">10.1038/s41477-023-01478-x</a>","mla":"Roychoudhry, S., et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” <i>Nature Plants</i>, vol. 9, Springer Nature, 2023, pp. 1500–13, doi:<a href=\"https://doi.org/10.1038/s41477-023-01478-x\">10.1038/s41477-023-01478-x</a>.","short":"S. Roychoudhry, K. Sageman-Furnas, C. Wolverton, P. Grones, S. Tan, G. Molnar, M. De Angelis, H. Goodman, N. Capstaff, L. JPB, J. Mullen, R. Hangarter, J. Friml, S. Kepinski, Nature Plants 9 (2023) 1500–1513.","ieee":"S. Roychoudhry <i>et al.</i>, “Antigravitropic PIN polarization maintains non-vertical growth in lateral roots,” <i>Nature Plants</i>, vol. 9. Springer Nature, pp. 1500–1513, 2023.","chicago":"Roychoudhry, S, K Sageman-Furnas, C Wolverton, Peter Grones, Shutang Tan, Gergely Molnar, M De Angelis, et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” <i>Nature Plants</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41477-023-01478-x\">https://doi.org/10.1038/s41477-023-01478-x</a>.","ista":"Roychoudhry S, Sageman-Furnas K, Wolverton C, Grones P, Tan S, Molnar G, De Angelis M, Goodman H, Capstaff N, JPB L, Mullen J, Hangarter R, Friml J, Kepinski S. 2023. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. 9, 1500–1513."},"file":[{"success":1,"relation":"main_file","date_updated":"2023-09-20T10:51:31Z","access_level":"open_access","file_size":9647103,"file_id":"14351","file_name":"2023_NaturePlants_Roychoudhry.pdf","checksum":"3d6d5d5abb937c14a5f6f0afba3b8624","date_created":"2023-09-20T10:51:31Z","content_type":"application/pdf","creator":"dernst"}],"abstract":[{"lang":"eng","text":"Lateral roots are typically maintained at non-vertical angles with respect to gravity. These gravitropic setpoint angles are intriguing because their maintenance requires that roots are able to effect growth response both with and against the gravity vector, a phenomenon previously attributed to gravitropism acting against an antigravitropic offset mechanism. Here we show how the components mediating gravitropism in the vertical primary root—PINs and phosphatases acting upon them—are reconfigured in their regulation such that lateral root growth at a range of angles can be maintained. We show that the ability of Arabidopsis lateral roots to bend both downward and upward requires the generation of auxin asymmetries and is driven by angle-dependent variation in downward gravitropic auxin flux acting against angle-independent upward, antigravitropic flux. Further, we demonstrate a symmetry in auxin distribution in lateral roots at gravitropic setpoint angle that can be traced back to a net, balanced polarization of PIN3 and PIN7 auxin transporters in the columella. These auxin fluxes are shifted by altering PIN protein phosphoregulation in the columella, either by introducing PIN3 phosphovariant versions or via manipulation of levels of the phosphatase subunit PP2A/RCN1. Finally, we show that auxin, in addition to driving lateral root directional growth, acts within the lateral root columella to induce more vertical growth by increasing RCN1 levels, causing a downward shift in PIN3 localization, thereby diminishing the magnitude of the upward, antigravitropic auxin flux."}],"title":"Antigravitropic PIN polarization maintains non-vertical growth in lateral roots","ddc":["580"],"oa_version":"Published Version","date_updated":"2024-10-21T06:01:33Z","day":"01","article_processing_charge":"Yes (in subscription journal)","date_published":"2023-09-01T00:00:00Z","status":"public","publication":"Nature Plants","publication_status":"published","author":[{"first_name":"S","full_name":"Roychoudhry, S","last_name":"Roychoudhry"},{"first_name":"K","full_name":"Sageman-Furnas, K","last_name":"Sageman-Furnas"},{"last_name":"Wolverton","full_name":"Wolverton, C","first_name":"C"},{"last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter","first_name":"Peter"},{"full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","orcid":"0000-0002-0471-8285","first_name":"Shutang"},{"full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Molnar","first_name":"Gergely"},{"first_name":"M","last_name":"De Angelis","full_name":"De Angelis, M"},{"first_name":"HL","full_name":"Goodman, HL","last_name":"Goodman"},{"full_name":"Capstaff, N","last_name":"Capstaff","first_name":"N"},{"last_name":"JPB","full_name":"JPB, Lloyd","first_name":"Lloyd"},{"first_name":"J","last_name":"Mullen","full_name":"Mullen, J"},{"first_name":"R","last_name":"Hangarter","full_name":"Hangarter, R"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"S","full_name":"Kepinski, S","last_name":"Kepinski"}],"date_created":"2023-09-15T09:56:01Z","department":[{"_id":"JiFr"}],"_id":"14339","has_accepted_license":"1","doi":"10.1038/s41477-023-01478-x","acknowledgement":"We thank D. Weijers, C. Schwechheimer and R. Offringa for generous sharing of published and unpublished materials and P. Masson for advice on the use of the ARL2 promoter. We are grateful to M. Del Bianco and O. Leyser for critical reading of the manuscript. This work was supported by the BBSRC (grants BB/N010124/1 and BB/R000859/1 to S.K.), the Gatsby Charitable Foundation and the Leverhulme Trust (RPG-2018-137 to S.K.).","scopus_import":"1","language":[{"iso":"eng"}],"file_date_updated":"2023-09-20T10:51:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"year":"2023"}]